I always separatre out the artifacts. The take from command works, and getting all the artifacts into a stocktpile can be quite useful. At least it means you know where they are.
But then I use the take from command a lot, since I try to build my forts with minimum transition goods supplies. basically I try to adopt "just in time" production proccesses with no unnecessary production. This instead of building warehousing.
So all goods are made with the intention of matching the demand, and stockpiles are normally only 3-5 squares and separated into input and output stockpiles next to relevant workshops. And each and every stockpile is configured to only accept the good that goes into that particular production chain.
This for instance allows to separate all inputs for quality, and shipping all low quality goods into dumping stockpiles which get regularily dumped into the magma chute. and finalized trade good production (after something has been crafted, embroided with masterwork quality cloth, masterfully cut dimond, adorned with silver and what not, and the trade depot is right next to the final workshop, and all the workshops are in a chain, with one assigned owner, who eats and lives in his own appartment above the workshop.
You would think that this would be extremly efficient, but the moving around, and reinstalling workshops and furniture, and keeping taps on all the production etc means that you always break the chain somewhere, idling all workshops below in the system. not to mention that no matter how hard you try, goods tend to get worked on in an irregular pattern due to sleep, eating and partying, and when one dwarf goes of to party, he doesn't produce output for the line line, breaking down the system again. etc...